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Two comments:
* This is wrong for i386 (at least under Debian): we should not restrict users to SSE or SSE2.
* About amd64, this bug is invalid (at least for the SSE). SSE is enabled by default under amd64 [1]http://gcc.gnu.org/onlinedocs/gcc/i386-and-x86_002d64-Options.html
`sse'
[...]
"This is the default choice for the x86-64 compiler."

Yes it is correct that for amd64 SSE is enabled by default in the compiler. But (if I'm not wrong) the FFTW --enable-sse flag does not (only) set compiler flags. Instead it activates the specially written SSE optimized kernels are compiled. Because the --enable-sse flag is not passed, those kernels are not compiled even though all amd64 processors have SSE/SSE2. Thus SSE is activated in the compiler but not for FFTW.

I'm one of the FFTW developers, and I can confirm that the SSE/SSE2 code is NOT compiled in FFTW if the --enable-sse/--enable-sse2 flags (in single/double precision) are omitted. You should definitely pass these flags to the configure script on x86-64 systems.

One other comment: it is save to use these flags on i386 - the resulting FFTW binary still works on machines not supporting SSE/SSE2, because it checks at runtime to see if SSE/SSE2 is available and disables FFTW's SSE/SSE2 routines if not.